Showing : Genomicranges • reset
1
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How to make combined annotation of 5'UTRs and CDS's?
annotation concatenation GRangesList GenomicRanges
6.6 years ago anmej • 0
0
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2
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1.2k
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feel confused when identifying overlapping regions by intersect method
GenomicRanges overlaps intersect
updated 6.7 years ago by ★ 11k • written 6.7 years ago by • 0
2
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1
reply
1.8k
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Create a matrix to show overlaps among multiple GRanges
r GRanges GenomicRanges
updated 6.7 years ago by 68k • written 6.7 years ago by ▴ 40
6
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8
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3.9k
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Ranges from a fasta file
biostrings fasta genomicranges granges
updated 6.7 years ago by 25k • written 6.7 years ago by ▴ 90
6
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12
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2.9k
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mclapply to loop over a GRangesList object
GenomicRanges GRanges GRangesList parallel mclapply
6.7 years ago foehn ▴ 100
0
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4
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2.4k
views
Unexpected behaviour of set operations on GRanges objects when dplyr is loaded
GenomicRanges S4Vectors dplyr
updated 6.8 years ago by 68k • written 6.8 years ago by ▴ 140
2
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2
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2.8k
views
Error in installation of scran
S4Vectors IRanges XVector GenomicRanges scran
updated 6.8 years ago by ★ 29k • written 6.8 years ago by • 0
4
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2
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1.5k
views
Speed efficient way to select the n-th element from GRangsList
R GenomicRanges IRanges
6.9 years ago foehn ▴ 100
0
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1
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1.1k
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How is it possible to override the constructor of the GRanges class?
genomicranges granges
6.9 years ago Shaurya Jauhari • 0
5
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8
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11k
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Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 3.7 years ago by • 0 • written 10.1 years ago by ▴ 50
0
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1
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1.6k
views
Subset bam file in R
rsamtools genomicalignments genomicranges
updated 6.9 years ago by ★ 11k • written 6.9 years ago by • 0
2
votes
1
reply
1.5k
views
Bug in follow and precede
software error genomicranges iranges
updated 6.9 years ago by ★ 6.8k • written 7.0 years ago by • 0
1
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2
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3.6k
views
How to convert bedgraph to wig
rtracklayer genomicranges
updated 6.9 years ago by ★ 11k • written 6.9 years ago by • 0
0
votes
7
replies
1.8k
views
rtracklayer cannot export empty BED file
rtracklayer bed genomicranges
updated 7.0 years ago by ★ 11k • written 7.0 years ago by ▴ 100
1
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1
reply
925
views
Bug report for GenomicRanges
genomicranges
updated 7.0 years ago by ★ 11k • written 7.0 years ago by ▴ 170
7
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5
replies
4.9k
views
summarize scores of GRanges into bins
genomicranges grangeslist bin findoverlaps
updated 7.0 years ago by • 0 • written 8.2 years ago by ★ 1.5k
0
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1
reply
844
views
How to find overlaps in genomic sequences comparing patients to themselves
genomicranges
7.1 years ago sbailey5 • 0
0
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2
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1.4k
views
Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
7.1 years ago A ▴ 60
0
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3
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1.7k
views
GenomicRanges based on indices or more conditions, and add column from match
genomicranges iranges findoverlaps
7.1 years ago francesca casalino ▴ 50
2
votes
1
reply
1.4k
views
Intra-range transformation on GPos-objects?
genomicranges gpos granges
updated 7.1 years ago by 16k • written 7.1 years ago by ▴ 180
0
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0
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1.8k
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GenomicFeatures: How to extract a gene's upstream region of TSS up to the end position of the flanking (nearby) gene.
genomicranges genomicfeatures promoter upstream_flank
7.1 years ago Wojeff • 0
2
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2
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5.1k
views
Concatenate a list of genomic ranges
r granges genomicranges
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
0
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2
replies
997
views
Error: the "phase" metadata column must contain 0, 1, or 2, for all the CDS features
genomicranges
7.2 years ago bbrink • 0
3
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3
replies
1.8k
views
Gaia results including negative widths
gaia genomicranges iranges
updated 7.2 years ago by ▴ 40 • written 7.2 years ago by ▴ 10
1
vote
1
reply
3.1k
views
Extracting gene structures from a GFF3 file for use with annotateWithGeneParts()
genomicfeatures genomation genomicranges methylation annotation
updated 7.3 years ago by ▴ 20 • written 7.3 years ago by • 0
0
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3
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1.4k
views
Nearest genomic ranges and distances in circular ranges
genomicranges
updated 7.3 years ago by ★ 6.8k • written 7.3 years ago by • 0
0
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3
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1.0k
views
'downstream' disappeared from GenomicRanges package?
genomicranges
7.3 years ago Vang Le ▴ 80
3
votes
2
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1.4k
views
Simplifying a RaggedExperiment using qreduceAssay and weighted means.
raggedexperiment genomicranges
updated 7.3 years ago by 25k • written 7.3 years ago by ★ 1.1k
5
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4
replies
2.7k
views
How do I do a bedtools like intersection in GenomicRanges?
genomicranges
updated 7.3 years ago by ★ 11k • written 7.3 years ago by ▴ 40
2
votes
12
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2.8k
views
nearest without overlapping
genomicranges
updated 7.4 years ago by 16k • written 7.4 years ago by ▴ 40
1
vote
5
replies
3.5k
views
Replacement for lapply on a GRanges?
genomicranges
updated 7.4 years ago by 16k • written 7.4 years ago by ▴ 890
7
votes
5
replies
2.6k
views
Strange error in bsseq when trying to assign seqinfo
bsseq genomeinfodb genomicranges seqinfo
written 7.5 years ago by ▴ 140
0
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1
reply
1.5k
views
GenomicRanges distanceToNearest: trouble replicating snp-gene mapping from older version
GenomicRanges distancetonearest strandedness
updated 7.6 years ago by ★ 6.8k • written 7.6 years ago by • 0
0
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1
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1.3k
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Detect Sites with Minimum Gap in GRanges Object
R genomicranges granges grange
7.6 years ago g.k • 0
2
votes
2
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1.2k
views
Features within 2kb window, but with resampling
genomicranges granges slidingwindow
updated 7.6 years ago by ★ 11k • written 7.6 years ago by • 0
3
votes
1
reply
1.0k
views
Finding the nearest n genes from a genomic loci
genomicranges
updated 7.6 years ago by ★ 11k • written 7.6 years ago by ▴ 20
1
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2
replies
1.6k
views
extending GenomicRanges::reduce warning, why ?
GenomicRanges reduce setMethod setGeneric
updated 7.7 years ago by 25k • written 7.7 years ago by ▴ 80
1
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3
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2.1k
views
How to operate on circular sequences with GenomicRanges?
GenomicRanges mitochondria circular
updated 7.7 years ago by ★ 6.8k • written 7.7 years ago by ▴ 120
3
votes
2
replies
2.5k
views
coverage() output SimpleRleList cannot be converted to GRanges
bug genomicranges granges rlelist coverage
updated 7.7 years ago by 16k • written 7.7 years ago by ▴ 10
0
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5
replies
1.4k
views
Problem converting annotation to GenomicRanges object
genomicranges
7.8 years ago Anton01 • 0
3
votes
4
replies
1.7k
views
Future plans for the new GPos class
genomicranges gpos
updated 7.8 years ago by 16k • written 7.8 years ago by ▴ 180
2
votes
8
replies
6.5k
views
GenomicRanges: identify overlapping regions, get intersection between each overlapping pair and add gene coordinates (start, end, strand and ids)
genomicranges overlap intersect findoverlaps
7.8 years ago Caroline Grisbach Meissner ▴ 10
2
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3
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1.9k
views
GRanges object from gene list
granges bed genomicranges genomeintervals deseq2
7.8 years ago rbronste ▴ 60
2
votes
4
replies
2.1k
views
Make window around TSS and get values from another data.frame for bins of the specified window
R granges genomicranges chipseq
updated 7.8 years ago by ★ 11k • written 7.8 years ago by ▴ 20
0
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0
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1.1k
views
coverage no longer works on GPos objects?
genomicranges gpos
7.8 years ago maltethodberg ▴ 180
1
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4
replies
4.4k
views
Generate 3' UTR and 5' UTR ranges from a gff file
gff genomicranges
updated 7.9 years ago by ★ 11k • written 7.9 years ago by ▴ 10
0
votes
6
replies
4.8k
views
GRanges::distanceToNearest does not return distance to nearest
granges genomicranges
updated 7.9 years ago by ★ 6.8k • written 7.9 years ago by ▴ 40
0
votes
1
reply
1.5k
views
Error when subsetting a RaggedExperiment by GenomicRanges
raggedexperiment genomicranges
updated 7.9 years ago by 700 • written 7.9 years ago by • 0
0
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1
reply
1.7k
views
GenomicRanges fails to load due to missing ngap method
software error genomicranges loadnamespace
updated 7.9 years ago by 25k • written 7.9 years ago by • 0
0
votes
2
replies
1.2k
views
GRangesList: wiered error
genomicranges genomicfeatures
7.9 years ago Fabian Grammes ▴ 20
403 results • Page 3 of 9
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Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
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Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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